DBNDD2

dysbindin domain containing 2

Basic information

Region (hg38): 20:45406056-45410610

Previous symbols: [ "C20orf35" ]

Links

ENSG00000244274 ∙ NCBI:55861 ∙ OMIM:611453 ∙ HGNC:15881 ∙ Uniprot:Q9BQY9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DBNDD2 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBNDD2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	16	0	0

Variants in DBNDD2

This is a list of pathogenic ClinVar variants found in the DBNDD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-45406480-T-G		not specified	Uncertain significance (Oct 03, 2022)
20-45406527-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-45406566-C-G		not specified	Uncertain significance (Sep 27, 2022)
20-45406590-C-T		not specified	Uncertain significance (Jan 06, 2023)
20-45406596-C-T		not specified	Uncertain significance (May 18, 2023)
20-45408173-G-C		not specified	Uncertain significance (Aug 04, 2023)
20-45408244-G-A		not specified	Uncertain significance (May 16, 2022)
20-45408322-C-T		not specified	Uncertain significance (Feb 23, 2023)
20-45408453-C-A		not specified	Uncertain significance (Oct 20, 2023)
20-45408463-C-A		not specified	Uncertain significance (Aug 17, 2021)
20-45408522-C-T		not specified	Uncertain significance (May 16, 2023)
20-45409935-T-C		not specified	Uncertain significance (Dec 03, 2021)
20-45409956-T-C		not specified	Uncertain significance (Apr 11, 2023)
20-45409979-G-A		not specified	Uncertain significance (Oct 14, 2023)
20-45409998-C-A		not specified	Uncertain significance (Mar 02, 2023)
20-45410018-G-T		not specified	Uncertain significance (Dec 07, 2021)
20-45410019-A-C		not specified	Uncertain significance (Dec 07, 2021)
20-45410032-C-A		not specified	Uncertain significance (Aug 03, 2022)
20-45410085-C-T		not specified	Uncertain significance (Sep 13, 2023)
20-45410127-G-C		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBNDD2	protein_coding	protein_coding	ENST00000372710	3	4554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00831	0.938	124782	0	10	124792	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.887	118	148	0.795	0.00000861	1681
Missense in Polyphen		42	59.115	0.71048		639
Synonymous	0.264	62	64.7	0.958	0.00000415	551
Loss of Function	1.67	5	11.0	0.456	6.36e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000353
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate the activity of casein kinase-1. Inhibits CSNK1D autophosphorylation (in vitro). {ECO:0000269|PubMed:16618118}.

Recessive Scores

• pRec: 0.0715

Haploinsufficiency Scores

• pHI: 0.0976
• hipred: N
• hipred_score: 0.146
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dbndd2
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; reproductive system phenotype

Gene ontology

• Biological process: negative regulation of protein kinase activity
• Cellular component: cytoplasm
• Molecular function: protein binding